Glycerol-derived ester oligomers from cork suberin

Suberin, the hallmark constituent of bark, identified in a 45-million-year-old monkeyhair tree (Coumoxylon hartigii) from Geiseltal, Germany

Suberin, a complex biopolymer, forms a water- and gas-insoluble barrier that protects the inner tissues of plants. It is abundant in tree bark, particularly in the cork oak Quercus suber. Anatomically, fossil bark has been described since the Devonian. However, its distinctive constituent suberin has not yet been reported from the fossil record. Here we present unambiguous chemical evidence for intact suberin from the bark of a middle Eocene monkeyhair tree from Geiseltal, eastern Germany. High-performance liquid chromatography coupled to electrospray ionization mass spectrometry (HPLC-ESI-MS) detected constituents of suberin in the outer layer the fossil monkeyhair tree, which confirms previous morphological interpretation of this tissue as bark, and chemically differentiates this layer from the two tissues of the inner layer. Notably, this is the first study with compelling chemical evidence for suberin in fossil bark. Fluorescence microspectroscopy additionally supports the presence of suberin. Fossilization conditions in the Eocene Geiseltal deposit were likely mild, with low moisture and temperatures, contributing to the remarkable preservation of bark and inner laticifer mats of the monkeyhair trees growing there 45 million years ago.

The Key Enzymes in the Suberin Biosynthetic Pathway in Plants: An Update

Suberin is a natural biopolymer found in a variety of specialized tissues, including seed coat integuments, root endodermis, tree bark, potato tuber skin and the russeted and reticulated skin of fruits. The suberin polymer consists of polyaliphatic and polyphenolic domains. The former is made of very long chain fatty acids, primary alcohols and a glycerol backbone, while the latter consists of p-hydroxycinnamic acid derivatives, which originate from the core phenylpropanoid pathway. In the current review, we survey the current knowledge on genes/enzymes associated with the suberin biosynthetic pathway in plants, reflecting the outcomes of considerable research efforts in the last two decades. We discuss the function of these genes/enzymes with respect to suberin aromatic and aliphatic monomer biosynthesis, suberin monomer transport, and suberin pathway regulation. We also delineate the consequences of the altered expression/accumulation of these genes/enzymes in transgenic plants.

Quantification of Structure-Property Relationships for Plant Polyesters Reveals Suberin and Cutin Idiosyncrasies

Polyesters, as they exist in planta, are promising materials with which to begin the development of "green" replacements. Cutin and suberin, polyesters found ubiquitously in plants, are prime candidates. Samples enriched for plant polyesters, and in which their native backbones were largely preserved, were studied to identify "natural" structural features; features that influence critical physical properties. Quantitative nuclear magnetic resonance (NMR), differential scanning calorimetry (DSC), and X-ray scattering methods were used to quantify structure-property relationships in these polymeric materials. The degree of esterification, namely, the presence of acylglycerol linkages in suberin and of secondary esters in cutin, and the existence of mid-chain epoxide groups defining the packing of the aliphatic chains were observed. This packing determines polymer crystallinity, the resulting crystal structure, and the melting temperature. To evaluate the strength of this rule, tomato cutin from the same genotype, studying wild-type plants and two well-characterized mutants, was analyzed. The results show that cutin's material properties are influenced by the amount of unbound aliphatic hydroxyl groups and by the length of the aliphatic chain. Collectively, the acquired data can be used as a tool to guide the selection of plant polyesters with precise structural features, and hence physicochemical properties.

Synthesis of 13 C-labelled ω-hydroxy carboxylic acids of the general formula HO2 13 C-(CH2 )n -CH2 OH or HO2 C-(CH2 )n -13 CH2 OH (n = 12, 16, 20, 28)

¹³ C-labelled ω-hydroxy-carboxylic acids HO₂ ¹³ C-(CH₂ )_n -CH₂ OH or HO₂ C-(CH₂ )_n -¹³ CH₂ OH (n = 12, 16, 20, 28) with ¹³ C labels selectively introduced either at the carboxy group or at the primary alcohol function at the end of the hydrocarbon chain have been synthesized. Different synthetic strategies had to be applied depending on the position of the label, the chain length of the respective synthetic target and due to economic considerations. ¹³ C labels in general were introduced by nucleophilic substitution of a suitable leaving group with labelled potassium cyanide and subsequent hydrolysis of the nitriles to produce the corresponding labelled carboxy functions, which may also be reduced to give the labelled primary alcohol group. All new compounds are characterized by GC/MS, IR and NMR methods as well as by elemental analysis.

Synthesis of 13 C-labelled cutin and suberin monomeric dicarboxylic acids of the general formula HO213 C-(CH2 )n -13 CO2 H (n = 10, 12, 14, 16, 18, 20, 22, 24, 26, 28)

13 C-labeled dicarboxylic acids HO213 C-(CH2 )n -13 CO2 H (n = 10, 12, 14, 16, 18, 20, 22, 24, 26, 28) have been synthesized as internal standards for LC-MS and GC-MS analysis of cutin and suberin monomer degradation by soil-based microorganisms. Different synthetic strategies had to be applied depending on the chain length of the respective synthetic target and because of economic considerations. 13 C-labels were introduced by nucleophilic substitution of a suitable leaving group with labelled potassium cyanide and subsequent hydrolysis of the nitriles to produce the corresponding dicarboxylic acids. All new compounds are characterized by GC/MS, IR, and NMR methods as well as by elemental analysis.

The sugarcane ShMYB78 transcription factor activates suberin biosynthesis in Nicotiana benthamiana

KEY MESSAGE

A sugarcane MYB present in the culm induces suberin biosynthesis and is involved both with fatty acid and phenolics metabolism. Few transcription factors have been described as regulators of cell wall polymers deposition in C4 grasses. Particularly, regulation of suberin biosynthesis in this group of plants remains poorly understood. Here, we showed that the sugarcane MYB transcription factor ShMYB78 is an activator of suberin biosynthesis and deposition. ShMYB78 was identified upon screening genes whose expression was upregulated in sugarcane internodes undergoing suberization during culm development or triggered by wounding. Agrobacterium-mediated transient expression of ShMYB78 in Nicotiana benthamiana leaves induced the ectopic deposition of suberin and its aliphatic and aromatic monomers. Further, the expression of suberin-related genes was induced by ShMYB78 heterologous expression in Nicotiana benthamiana leaves. ShMYB78 was shown to be a nuclear protein based on its presence in sugarcane internode nuclear protein extracts, and protoplast transactivation assays demonstrated that ShMYB78 activates the promoters of the sugarcane suberin biosynthetic genes β-ketoacyl-CoA synthase (ShKCS20) and caffeic acid-O-methyltransferase (ShCOMT). Our results suggest that ShMYB78 may be involved in the transcriptional regulation of suberin deposition, from fatty acid metabolism to phenylpropanoid biosynthesis, in sugarcane internodes.

An untargeted liquid chromatography-mass spectrometry-based workflow for the structural characterization of plant polyesters

Cell wall localized heterogeneous polyesters are widespread in land plants. The composition of these polyesters, such as cutin, suberin, or more plant-specific forms such as the flax seed coat lignan macromolecule, can be determined after total hydrolysis of the ester linkages. The main bottleneck in the structural characterization of these macromolecules, however, resides in the determination of the higher order monomer sequences. Partial hydrolysates of the polyesters release a complex mixture of fragments of different lengths, each present in low abundance and therefore are challenging to structurally characterize. Here, a method is presented by which liquid chromatography-mass spectrometry (LC-MS) profiles of such partial hydrolysates are searched for pairs of related fragments. LC-MS peaks that show a mass difference corresponding to the addition of one or more macromolecule monomers were connected in a network. Starting from the lowest molecular weight peaks in the network, the annotation of the connections as the addition of one or more polyester monomers allows the prediction of consecutive and increasingly complex adjacent peaks. Multi-stage MS (MSn) experiments further helped to reject, corroborate, and sometimes refine the structures predicted by the network. As a proof of concept, this procedure was applied to partial hydrolysates of the flax seed coat lignan macromolecule, and allowed to characterize 120 distinct oligo-esters, consisting of up to six monomers, and containing monomers and linkages for which incorporation in the lignan macromolecule had not been described before. These results showed the capacity of the approach to advance the structural elucidation of complex plant polyesters.

A methodological approach for the simultaneous quantification of glycerol and fatty acids from cork suberin in a single GC run

INTRODUCTION

Suberin, as part of plant protective barriers, is one of the most important natural polymers after cellulose and lignin. For a full elucidation of suberin structure the quantification of glycerol, fatty α,ω-diacids and ω-hydroxyacids, the major building blocks of suberin, is of primary importance. Glycerol is often lost in the most used analytical procedures or rarely determined by deficient or too laborious techniques.

OBJECTIVES

Propose a simple, accessible and reliable methanolysis work-up procedure for an accurate and simultaneous quantification of glycerol and suberin fatty monomers in the same GC run.

MATERIAL AND METHODS

Cork from Quercus suber L. was depolymerised by methanolysis. Glycerol was derivatised to an organic soluble form before the suberin monomers recovery in water/organic solvent partition. Gas chromatography flame ionisation detector (GC-FID) response factors were determined for glycerol, ferulic acid and one for each fatty monomer substructure. Additionally, 1,2,4-butanetriol and methyl nonadecanoate were used as internal standards.

RESULTS

The proposed experimental approach allowed the glycerol and all the fatty suberin monomers in the same GC run to be quantified accurately. Glycerol represented 30.6 area%, 14.2 mass% and 38.4 molar% of suberin and the COOH/OH groups ratio was 0.6:1 in the proposed experimental approach in contrast with 0.10 area% and COOH/OH ratio of 3:1 in the most used protocol. Furthermore, ω-hydroxyacids/α,ω-diacids mass ratio was 1:1 as opposed to an area ratio of 1.5:1.

CONCLUSION

The proposed work-up procedure revealed to be a reliable analytical tool for the complete analysis of suberin allowing the future knowledge to grow towards a better understanding of suberin structure throughout its range and variability.

Structure and Properties of Cork-Silica Xerogel Nanocomposites: Influence of the Cork Content

Environmentally friendly nanocomposites were synthesized from a silica precursor and cork under mild conditions and dried at atmospheric pressure. Because of the covalent bonding between the components, these CorSil nanocomposites are homogeneous, light (apparent density in the range 360-750 kg m^-3), machinable, with the Shore D hardness up to 67 and compressive strength up to 22.6 MPa. These properties place them as good replacements for wood, other natural products, and thermoplastic polymers, with the advantage of being flame-retardant. The influence of the cork content and grain size on the structure, porosity, and mechanical properties of the nanocomposites was studied using infrared spectroscopy, sorption isotherms, compressive strength, and Shore D hardness measurements.

ChIP-Seq reveals that QsMYB1 directly targets genes involved in lignin and suberin biosynthesis pathways in cork oak (Quercus suber)

BACKGROUND

Gene activity is largely controlled by transcriptional regulation through the action of transcription factors and other regulators. QsMYB1 is a member of the R2R3-MYB transcription factor family related to secondary growth, and in particular, with the cork development process. In order to identify the putative gene targets of QsMYB1 across the cork oak genome we developed a ChIP-Seq strategy.

RESULTS

Results provide direct evidence that QsMY1B targets genes encoding for enzymes involved in the lignin and suberin pathways as well as gene encoding for ABCG transporters and LTPs implicated in the transport of monomeric suberin units across the cellular membrane. These results highlight the role of QsMYB1 as a regulator of lignin and suberin biosynthesis, transport and assembly.

CONCLUSION

To our knowledge, this work constitutes the first ChIP-Seq experiment performed in cork oak, a non-model plant species with a long-life cycle, and these results will contribute to deepen the knowledge about the molecular mechanisms of cork formation and differentiation.

Quantitative analysis of glycerol in dicarboxylic acid-rich cutins provides insights into Arabidopsis cutin structure

Cutin is an extracellular lipid polymer that contributes to protective cuticle barrier functions against biotic and abiotic stresses in land plants. Glycerol has been reported as a component of cutin, contributing up to 14% by weight of total released monomers. Previous studies using partial hydrolysis of cuticle-enriched preparations established the presence of oligomers with glycerol-aliphatic ester links. Furthermore, glycerol-3-phosphate 2-O-acyltransferases (sn-2-GPATs) are essential for cutin biosynthesis. However, precise roles of glycerol in cutin assembly and structure remain uncertain. Here, a stable isotope-dilution assay was developed for the quantitative analysis of glycerol by GC/MS of triacetin with simultaneous determination of aliphatic monomers. To provide clues about the role of glycerol in dicarboxylic acid (DCA)-rich cutins, this methodology was applied to compare wild-type (WT) Arabidopsis cutin with a series of mutants that are defective in cutin synthesis. The molar ratio of glycerol to total DCAs in WT cutins was 2:1. Even when allowing for a small additional contribution from hydroxy fatty acids, this is a substantially higher glycerol to aliphatic monomer ratio than previously reported for any cutin. Glycerol content was strongly reduced in both stem and leaf cutin from all Arabidopsis mutants analyzed (gpat4/gpat8, att1-2 and lacs2-3). In addition, the molar reduction of glycerol was proportional to the molar reduction of total DCAs. These results suggest "glycerol-DCA-glycerol" may be the dominant motif in DCA-rich cutins. The ramifications and caveats for this hypothesis are presented.

Functional testing of a PF02458 homologue of putative rice arabinoxylan feruloyl transferase genes in Brachypodium distachyon

We show that changing the expression of a putative feruloyl transferase gene belonging to the BAHD acyl-transferase family alters the levels of cell wall esterified ferulates and diferulates in Brachypodium distachyon cell walls. While the potential of grass cell walls for biofuel production has been realized, the technology for lignocellulosic biomass conversion for the production of ethanol is still inefficient because of structural mechanisms that plants have evolved to make the cell wall recalcitrant to enzymatic attack. One of these mechanisms in grasses involves the esterification of arabinoxylans in the cell wall with ferulic acid via an ester linkage to arabinose side chains on xylans. These ferulates undergo oxidative coupling reactions to form ferulate dimers, thus crosslinking polysaccharides. Arabinoxylan feruloylation is an important factor that determines cell wall recalcitrance because it directly cross-links xylans and because ferulates act as nucleating sites for the formation of lignin and for the linkage of lignin to the xylan/cellulose network. Here we report on the effects of changing the expression of Bradi2g43520 (BdAT1), a homologue of the rice feruloyl transferase gene Os01g42880 belonging to the Pfam PF02458 family, in Brachypodium distachyon. Down regulation in several independent RNAi::BdAT1 lines, resulted in up to a 35 % reduction of ferulate levels in both leaves and stems compared to control plants, over 2-3 generations of selfing. In contrast, overexpression of putative BdAT1 resulted in an increase of up to 58 and 47 % of ferulate levels in leaves and stems, respectively, compared to control plants and analyzed over 2-3 generations of selfing. These findings suggest that Bradi2g43520 may be a good candidate for feruloylation of AX in Brachypodium.

Suberin: the biopolyester at the frontier of plants

Suberin is a lipophilic macromolecule found in specialized plant cell walls, wherever insulation or protection toward the surroundings is needed. Suberized cells form the periderm, the tissue that envelops secondary stems as part of the bark, and develop as the sealing tissue after wounding or leaf abscission. Suberin is a complex polyester built from poly-functional long-chain fatty acids (suberin acids) and glycerol. The suberin acids composition of a number of plant tissues and species is now established, but how the polyester macromolecule is assembled within the suberized cell walls is not known. In the last years contributions from several areas have however significantly enriched our understanding of suberin. The primary structure of the polyester, i.e., how the suberin acids and glycerol are sequentially linked was revealed, together with the stereochemistry of the mid-chain functional groups some suberin acids have; solid-state NMR studies showed the presence of methylene chains spatially separated and with different molecular mobility; biophysical studies showed the membrane behavior of suberin acids derivatives, allowing new insights on structure-properties relationships; and a number of candidate genes were conclusively related to suberin biosynthesis. The comprehension of suberin as a macromolecule will be essential to understand its vital protective roles in plants and how they will deal with eventual environmental changes. Suberin is also expected to be a source for high-performing bio-based chemicals, taking advantage of the structural uniqueness of their constituent suberin acids.

Suberin: biosynthesis, regulation, and polymer assembly of a protective extracellular barrier

Suberin is a lipid-phenolic biopolyester deposited in the cell walls of certain boundary tissue layers of plants, such as root endodermis, root and tuber peridermis, and seed coats. Suberin serves as a protective barrier in these tissue layers, controlling, for example, water and ion transport. It is also a stress-induced anti-microbial barrier. The suberin polymer contains a variety of C16-C24 chain-length aliphatics, such as ω-hydroxy fatty acids, α,ω-dicarboxylic fatty acids, and primary fatty alcohols. Suberin also contains high amounts of glycerol and phenolics, especially ferulic acid. In addition, non-covalently linked waxes are likely associated with the suberin polymer. This review focusses on the suberin biosynthetic enzymes identified to date, which include β-ketoacyl-CoA synthases, fatty acyl reductases, long-chain acyl-CoA synthetases, cytochrome P450 monooxygenases, glycerol 3-phosphate acyltransferases, and phenolic acyltransferases. We also discuss recent advances in our understanding of the transport of suberin components intracellularly and to the cell wall, polymer assembly, and the regulation of suberin deposition.

AtMYB41 activates ectopic suberin synthesis and assembly in multiple plant species and cell types

Suberin is a lipid and phenolic cell wall heteropolymer found in the roots and other organs of all vascular plants. Suberin plays a critical role in plant water relations and in protecting plants from biotic and abiotic stresses. Here we describe a transcription factor, AtMYB41 (At4g28110), that can activate the steps necessary for aliphatic suberin synthesis and deposition of cell wall-associated suberin-like lamellae in both Arabidopsis thaliana and Nicotiana benthamiana. Overexpression of AtMYB41 increased the abundance of suberin biosynthetic gene transcripts by orders of magnitude and resulted in the accumulation of up to 22 times more suberin-type than cutin-type aliphatic monomers in leaves. Overexpression of AtMYB41 also resulted in elevated amounts of monolignols in leaves and an increase in the accumulation of phenylpropanoid and lignin biosynthetic gene transcripts. Surprisingly, ultrastructural data indicated that overexpression led to the formation of suberin-like lamellae in both epidermal and mesophyll cells of leaves. We further implicate AtMYB41 in the production of aliphatic suberin under abiotic stress conditions. These results provide insight into the molecular-genetic mechanisms of the biosynthesis and deposition of a ubiquitous cell wall-associated plant structure and will serve as a basis for discovering the transcriptional network behind one of the most abundant lipid-based polymers in nature.

Apoplastic diffusion barriers in Arabidopsis

During the development of Arabidopsis and other land plants, diffusion barriers are formed in the apoplast of specialized tissues within a variety of plant organs. While the cuticle of the epidermis is the primary diffusion barrier in the shoot, the Casparian strips and suberin lamellae of the endodermis and the periderm represent the diffusion barriers in the root. Different classes of molecules contribute to the formation of extracellular diffusion barriers in an organ- and tissue-specific manner. Cutin and wax are the major components of the cuticle, lignin forms the early Casparian strip, and suberin is deposited in the stage II endodermis and the periderm. The current status of our understanding of the relationships between the chemical structure, ultrastructure and physiological functions of plant diffusion barriers is discussed. Specific aspects of the synthesis of diffusion barrier components and protocols that can be used for the assessment of barrier function and important barrier properties are also presented.

Acyl-lipid metabolism

Acyl lipids in Arabidopsis and all other plants have a myriad of diverse functions. These include providing the core diffusion barrier of the membranes that separates cells and subcellular organelles. This function alone involves more than 10 membrane lipid classes, including the phospholipids, galactolipids, and sphingolipids, and within each class the variations in acyl chain composition expand the number of structures to several hundred possible molecular species. Acyl lipids in the form of triacylglycerol account for 35% of the weight of Arabidopsis seeds and represent their major form of carbon and energy storage. A layer of cutin and cuticular waxes that restricts the loss of water and provides protection from invasions by pathogens and other stresses covers the entire aerial surface of Arabidopsis. Similar functions are provided by suberin and its associated waxes that are localized in roots, seed coats, and abscission zones and are produced in response to wounding. This chapter focuses on the metabolic pathways that are associated with the biosynthesis and degradation of the acyl lipids mentioned above. These pathways, enzymes, and genes are also presented in detail in an associated website (ARALIP: http://aralip.plantbiology.msu.edu/). Protocols and methods used for analysis of Arabidopsis lipids are provided. Finally, a detailed summary of the composition of Arabidopsis lipids is provided in three figures and 15 tables.

Solving the puzzles of cutin and suberin polymer biosynthesis

Cutin and suberin are insoluble lipid polymers that provide critical barrier functions to the cell wall of certain plant tissues, including the epidermis, endodermis and periderm. Genes that are specific to the biosynthesis of cutins and/or aliphatic suberins have been identified, mainly in Arabidopsis thaliana. They notably encode acyltransferases, oxidases and transporters, which may have either well-defined or more debatable biochemical functions. However, despite these advances, important aspects of cutin and suberin synthesis remain obscure. Central questions include whether fatty acyl monomers or oligomers are exported, and the extent of extracellular assembly and attachment to the cell wall. These issues are reviewed. Greater emphasis on chemistry and biochemistry will be required to solve these unknowns and link structure with function.

Suberin research in the genomics era--new interest for an old polymer

Suberin is an apoplastic biopolymer with tissue-specific deposition in the cell walls of the endo- and exodermis of roots, of periderms including wound periderm and other border tissues. Suberised cell walls contain both polyaliphatic and polyaromatic domains which are supposedly cross-linked. The predominant aliphatic components are ω-hydroxyacids, α,ω-diacids, fatty acids and primary alcohols, whereas hydroxycinnamic acids, especially ferulic acid, are the main components of the polyaromatic domain. Although the monomeric composition of suberin has been known for decades, its biosynthesis and deposition has mainly been a subject of speculation. Only recently, significant progress elucidating suberin biosynthesis has been achieved using molecular genetic approaches, especially in the model species Arabidopsis. In parallel, the long-standing hypothesis that suberin functions as an apoplastic barrier has been corroborated by sophisticated, quantitative physiological studies in the past decade. These studies demonstrated that suberised cell walls could act as barriers, minimising the movement of water and nutrients, restricting pathogen invasion and impeding toxic gas diffusion. In addition, suberised cell walls provide a barrier to radial oxygen loss from roots to the anaerobic root substrate in wetland plants. The recent onset of multidisciplinary approaches combining genetic, analytical and physiological studies has begun to deliver further insights into the physiological importance of suberin depositions in plants.

Linear and branched poly(omega-hydroxyacid) esters in plant cutins

Poly(omega-hydroxyacid) ester oligomers were obtained from the cutin of four plant cuticles by partial depolymerization methanolysis. The structure of these oligomers was determined by electrospray ionization coupled to tandem mass spectrometry (ESI-MS/MS) analysis of their lithium-adducts, showing which monomers were present and their relative position. Dimers up to heptamers were identified, in a total yield of oligomers of up to 50% of the total cutin content. Two main structural types of poly(omega-hydroxyacid) ester oligomers were found. Poly(10,16-dihydroxyhexadecanoic acid) esters were the main oligomers in the cutin of Lycopersicum esculentum fruit, with a predominantly branched structure. The 1D and 2D NMR analysis of these oligomers showed that inter-monomer linkages were mostly in secondary midchain hydroxyls, in a ratio of 4.5 to 1, compared with esterification in the primary omega-hydroxyls. In Hedera helix leaves cutin, poly(9-epoxy-18-hydroxyoctadecanoic acid) esters were the dominant oligomers, composed of monomers linearly linked head-to-tail. It is proposed that the cutin polyesters have different poly(omega-hydroxyacid)ester domains, either built of linear chains, where the C18-epoxy omega-hydroxyacids are dominant, or forming a highly branched network, where the C16-dihydroxy omega-hydroxyacids predominate. It is hypothesized that the C18 linear polyester can account for the ordered lamellae seen at ultrastructural level in H. helix cuticle, and that the C16 mostly branched polyester will be the basis of the reticulate structure seen in L. esculentum cuticle.

Three Arabidopsis fatty acyl-coenzyme A reductases, FAR1, FAR4, and FAR5, generate primary fatty alcohols associated with suberin deposition

Suberin is a protective hydrophobic barrier consisting of phenolics, glycerol, and a variety of fatty acid derivatives, including C18:0-C22:0 primary fatty alcohols. An eight-member gene family encoding alcohol-forming fatty acyl-coenzyme A reductases (FARs) has been identified in Arabidopsis (Arabidopsis thaliana). Promoter-driven expression of the beta-glucuronidase reporter gene indicated that three of these genes, FAR1(At5g22500), FAR4(At3g44540), and FAR5(At3g44550), are expressed in root endodermal cells. The three genes were transcriptionally induced by wounding and salt stress. These patterns of gene expression coincide with known sites of suberin deposition. We then characterized a set of mutants with T-DNA insertions in FAR1, FAR4, or FAR5 and found that the suberin compositions of roots and seed coats were modified in each far mutant. Specifically, C18:0-OH was reduced in far5-1, C20:0-OH was reduced in far4-1, and C22:0-OH was reduced in far1-1. We also analyzed the composition of polymer-bound lipids of leaves before and after wounding and found that the basal levels of C18:0-C22:0 primary alcohols in wild-type leaves were increased by wounding. In contrast, C18:0-OH and C22:0-OH were not increased by wounding in far5-1 and far1-1 mutants, respectively. Heterologous expression of FAR1, FAR4, and FAR5 in yeast confirmed that they are indeed active alcohol-forming FARs with distinct, but overlapping, chain length specificities ranging from C18:0 to C24:0. Altogether, these results indicate that Arabidopsis FAR1, FAR4, and FAR5 generate the fatty alcohols found in root, seed coat, and wound-induced leaf tissue.

Acyl-lipid metabolism

Acyl lipids in Arabidopsis and all other plants have a myriad of diverse functions. These include providing the core diffusion barrier of the membranes that separates cells and subcellular organelles. This function alone involves more than 10 membrane lipid classes, including the phospholipids, galactolipids, and sphingolipids, and within each class the variations in acyl chain composition expand the number of structures to several hundred possible molecular species. Acyl lipids in the form of triacylglycerol account for 35% of the weight of Arabidopsis seeds and represent their major form of carbon and energy storage. A layer of cutin and cuticular waxes that restricts the loss of water and provides protection from invasions by pathogens and other stresses covers the entire aerial surface of Arabidopsis. Similar functions are provided by suberin and its associated waxes that are localized in roots, seed coats, and abscission zones and are produced in response to wounding. This chapter focuses on the metabolic pathways that are associated with the biosynthesis and degradation of the acyl lipids mentioned above. These pathways, enzymes, and genes are also presented in detail in an associated website (ARALIP: http://aralip.plantbiology.msu.edu/). Protocols and methods used for analysis of Arabidopsis lipids are provided. Finally, a detailed summary of the composition of Arabidopsis lipids is provided in three figures and 15 tables.

A hydroxycinnamoyltransferase responsible for synthesizing suberin aromatics in Arabidopsis

Suberin, a polyester polymer in the cell wall of terrestrial plants, controls the transport of water and nutrients and protects plant from pathogenic infections and environmental stresses. Structurally, suberin consists of aliphatic and aromatic domains; p-hydroxycinnamates, such as ferulate, p-coumarate, and/or sinapate, are the major phenolic constituents of the latter. By analyzing the "wall-bound" phenolics of mutant lines of Arabidopsis deficient in a family of acyl-CoA dependent acyltransferase (BAHD) genes, we discovered that the formation of aromatic suberin in Arabidopsis, primarily in seed and root tissues, depends on a member of the BAHD superfamily of enzymes encoded by At5g41040. This enzyme exhibits an omega-hydroxyacid hydroxycinnamoyltransferase activity with an in vitro kinetic preference for feruloyl-CoA and 16-hydroxypalmitic acid. Knocking down or knocking out the At5g41040 gene in Arabidopsis reduces specifically the quantity of ferulate in suberin, but does not affect the accumulation of p-coumarate or sinapate. The loss of the suberin phenolic differentially affects the aliphatic monomer loads and alters the permeability and sensitivity of seeds and roots to salt stress. This highlights the importance of suberin aromatics in the polymer's function.

Identification of an Arabidopsis feruloyl-coenzyme A transferase required for suberin synthesis

All plants produce suberin, a lipophilic barrier of the cell wall that controls water and solute fluxes and restricts pathogen infection. It is often described as a heteropolymer comprised of polyaliphatic and polyaromatic domains. Major monomers include omega-hydroxy and alpha,omega-dicarboxylic fatty acids, glycerol, and ferulate. No genes have yet been identified for the aromatic suberin pathway. Here we demonstrate that Arabidopsis (Arabidopsis thaliana) gene AT5G41040, a member of the BAHD family of acyltransferases, is essential for incorporation of ferulate into suberin. In Arabidopsis plants transformed with the AT5G41040 promoter:YFP fusion, reporter expression is localized to cell layers undergoing suberization. Knockout mutants of AT5G41040 show almost complete elimination of suberin-associated ester-linked ferulate. However, the classic lamellar structure of suberin in root periderm of at5g41040 is not disrupted. The reduction in ferulate in at5g41040-knockout seeds is associated with an approximate stoichiometric decrease in aliphatic monomers containing omega-hydroxyl groups. Recombinant AT5G41040p catalyzed acyl transfer from feruloyl-coenzyme A to omega-hydroxyfatty acids and fatty alcohols, demonstrating that the gene encodes a feruloyl transferase. CYP86B1, a cytochrome P450 monooxygenase gene whose transcript levels correlate with AT5G41040 expression, was also investigated. Knockouts and overexpression confirmed CYP86B1 as an oxidase required for the biosynthesis of very-long-chain saturated alpha,omega-bifunctional aliphatic monomers in suberin. The seed suberin composition of cyp86b1 knockout was surprisingly dominated by unsubstituted fatty acids that are incapable of polymeric linkages. Together, these results challenge our current view of suberin structure by questioning both the function of ester-linked ferulate as an essential component and the existence of an extended aliphatic polyester.

A hydroxycinnamoyltransferase responsible for synthesizing suberin aromatics in Arabidopsis

Suberin, a polyester polymer in the cell wall of terrestrial plants, controls the transport of water and nutrients and protects plant from pathogenic infections and environmental stresses. Structurally, suberin consists of aliphatic and aromatic domains; p-hydroxycinnamates, such as ferulate, p-coumarate, and/or sinapate, are the major phenolic constituents of the latter. By analyzing the "wall-bound" phenolics of mutant lines of Arabidopsis deficient in a family of acyl-CoA dependent acyltransferase (BAHD) genes, we discovered that the formation of aromatic suberin in Arabidopsis, primarily in seed and root tissues, depends on a member of the BAHD superfamily of enzymes encoded by At5g41040. This enzyme exhibits an omega-hydroxyacid hydroxycinnamoyltransferase activity with an in vitro kinetic preference for feruloyl-CoA and 16-hydroxypalmitic acid. Knocking down or knocking out the At5g41040 gene in Arabidopsis reduces specifically the quantity of ferulate in suberin, but does not affect the accumulation of p-coumarate or sinapate. The loss of the suberin phenolic differentially affects the aliphatic monomer loads and alters the permeability and sensitivity of seeds and roots to salt stress. This highlights the importance of suberin aromatics in the polymer's function.

Building lipid barriers: biosynthesis of cutin and suberin

Cutin and suberin are the polymer matrices for lipophilic cell wall barriers. These barriers control the fluxes of gases, water and solutes, and also play roles in protecting plants from biotic and abiotic stresses and in controlling plant morphology. Although they are ubiquitous, cutin and suberin are the least understood of the major plant extracellular polymers. The use of forward and reverse genetic approaches in Arabidopsis has led to the identification of oxidoreductase and acyltransferase genes involved in the biosynthesis of these polymers. However, major questions about the underlying polymer structure, biochemistry, and intracellular versus extracellular assembly remain to be resolved. The analysis of plant lines with modified cutins and suberins has begun to reveal the inter-relationships between the composition and function of these polymers.

Suberin--a biopolyester forming apoplastic plant interfaces

Suberized cell walls form physiologically important plant-environment interfaces because they act as barriers that limit water and nutrient transport and protect plants from invasion by pathogens. Plants respond to environmental stimuli by modifying the degree of suberization in root cell walls. Salt stress or drought-induced suberization leads to a decrease in radial water transport in roots. Although reinforced, suberized cell walls never act as absolutely impermeable barriers. Deeper insights into the structure and biosynthesis of suberin are required to elucidate what determines the barrier properties. Progress has been obtained from analytical methods that enabled the structural characterization of oligomeric building blocks in suberin, and from the opening of suberin research to molecular genetic approaches by the elucidation of the chemical composition and tissue distribution of suberin in the model species Arabidopsis.

Suberin: A Biopolyester of Plants' Skin

Suberin is a biopolymer that acts as a barrier between plants and the environment. It is known to be a complex polyester based on glycerol and long-chain alpha,omega-diacids and omega-hydroxyacids. How these monomeric units are assembled at a macromolecular level remains mostly unknown. The knowledge gathered in the last 10 years has opened new insights into suberin structure. Suberin oligomeric blocks have been obtained after the partial depolymerization of the biopolymer, and in-situ studies by solid-state (13)C NMR spectroscopy have shown different molecular domains and how they are spatially related. Based on these latter developments, a model is proposed for the suberin macromolecular structure. The uniqueness of the suberin polyester opens perspectives for its use as a source of bio-based materials.